DHCR24 p.Phe46=
c.138C>T · rs747179972 · VCV1909866
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.004%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.2 | GERP 0.72, phastCons 1 |
| Overall | ||
| CADD | 18.74 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.004%
African / African-American · 3/74,918 alleles
Filtering AF
0.00259%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00233%
Overall
0.00297%
48/1,613,626 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.004% | 24,973 |
| European (non-Finnish) | 0.00348% | 28,775 |
| Admixed American | 0.00333% | 30,001 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,223 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- DHCR24
- Protein
- p.Phe46=
- Coding
- c.138C>T
- MANE Select
- NM_014762
- dbSNP
- rs747179972
- Type
- single nucleotide variant
- Location
- chr1:54886982 (GRCh38)
- Gene constraint
- LOEUF 0.597 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 92.40
Similar variants
- DHCR24 c.1218+1G>A Pathogenic/Likely pathogenic ★★ same type
- DHCR24 p.Glu191Lys Likely pathogenic ★★ same type
- DHCR24 c.*1424C>T Uncertain significance ★★ same type
- DHCR24 c.*2514A>G Uncertain significance ★★ same type
- DHCR24 p.Ala227Thr Uncertain significance ★★ ⚠ same type
- DHCR24 p.Arg132His Uncertain significance ★★ ⚠ same type
- DHCR24 p.Arg230Cys Uncertain significance ★★ ⚠ same type
- DHCR24 p.Arg230His Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dhcr24-p-phe46 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown